BLANCHET Christophe (6497bd49) at 28 Mar 16:39
Add Jupyter configuration from a remote tarball.
... and 1 more commit
BLANCHET Christophe (2c90ac56) at 27 Mar 17:38
Clean remaining debug config.
La connexion a échoué.
Pas d'erreur de déploiement remontée.
Test VM 29310
(base) jovyan@855551eeb996:~$ ls *
ifbdata:
ifb_core mydatalocal public
work:
testfile
BLANCHET Christophe (f54a1b33) at 27 Mar 17:12
Add Jupyter configuration from a git repository.
... and 1 more commit
L'utilisation de micromamba
résoud le problème.
https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html
Test VM 29257
L'activation de conda base
interfère avec le client slipstream
.
install.sh
# Install snakemake nextflow
echo "Install SnakeMake, Nextflow (with Conda/Mamba)"
conda activate base
${MAMBA_BIN} create -y -c conda-forge -c bioconda -n nextflow nextflow
${MAMBA_BIN} create -y -c conda-forge -c bioconda -n snakemake snakemake
conda deactivate
/var/log/slipstream/client/machine.slipstream.log
Using mamba.
Install SnakeMake, Nextflow (with Conda/Mamba)
Traceback (most recent call last):
File "/var/lib/miniforge/bin/mamba", line 7, in <module>
from mamba.mamba import main
File "/var/lib/miniforge/lib/pypy3.9/site-packages/mamba/mamba.py", line 16, in <module>
from conda.cli.common import check_non_admin, confirm_yn, specs_from_url
File "/var/lib/miniforge/lib/pypy3.9/site-packages/conda/cli/common.py", line 16, in <module>
from ..exceptions import (
File "/var/lib/miniforge/lib/pypy3.9/site-packages/conda/exceptions.py", line 16, in <module>
from requests.exceptions import JSONDecodeError
ImportError: cannot import name 'JSONDecodeError' from 'requests.exceptions' (/opt/slipstream/client/lib/requests/exceptions.py)
BLANCHET Christophe (47690c2e) at 25 Mar 10:50
Fix Napari install (#4).
BLANCHET Christophe (6b281756) at 25 Mar 10:37
MAMBA_ROOT_PREFIX must be a global variable (#2).
BLANCHET Christophe (978312ba) at 25 Mar 08:26
Use micromamba to install napari conda env (#4).
BLANCHET Christophe (a2230a2a) at 25 Mar 08:09
Get conda root prefix from IFB profile (#2).
BLANCHET Christophe (c7f81c5f) at 25 Mar 08:08
Record conda root prefix in IFB profile (ifb-biosphere/apps/biopipe...
Erreur avec la commande conda
dans install.sh
.
CONDA_ROOT_PREFIX=$( conda info -q --base )
Traceback (most recent call last):
File "/var/lib/miniforge/lib/pypy3.9/site-packages/conda/exception_handler.py", line 17, in __call__
return func(*args, **kwargs)
File "/var/lib/miniforge/lib/pypy3.9/site-packages/conda/cli/main.py", line 51, in main_subshell
from .conda_argparse import do_call, generate_parser, generate_pre_parser
File "/var/lib/miniforge/lib/pypy3.9/site-packages/conda/cli/conda_argparse.py", line 50, in <module>
from .main_create import configure_parser as configure_parser_create
File "/var/lib/miniforge/lib/pypy3.9/site-packages/conda/cli/main_create.py", line 11, in <module>
from ..notices import notices
File "/var/lib/miniforge/lib/pypy3.9/site-packages/conda/notices/__init__.py", line 3, in <module>
from .core import notices # noqa: F401
File "/var/lib/miniforge/lib/pypy3.9/site-packages/conda/notices/core.py", line 14, in <module>
from . import cache, fetch, views
File "/var/lib/miniforge/lib/pypy3.9/site-packages/conda/notices/cache.py", line 25, in <module>
from ..utils import ensure_dir_exists
File "/var/lib/miniforge/lib/pypy3.9/site-packages/conda/utils.py", line 23, in <module>
from .gateways.disk.read import compute_sum
File "/var/lib/miniforge/lib/pypy3.9/site-packages/conda/gateways/disk/read.py", line 31, in <module>
from ...exceptions import CondaUpgradeError, CondaVerificationError, PathNotFoundError
File "/var/lib/miniforge/lib/pypy3.9/site-packages/conda/exceptions.py", line 16, in <module>
from requests.exceptions import JSONDecodeError
ImportError: cannot import name 'JSONDecodeError' from 'requests.exceptions' (/opt/slipstream/client/lib/requests/exceptions.py)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/var/lib/miniforge/bin/conda", line 13, in <module>
sys.exit(main())
File "/var/lib/miniforge/lib/pypy3.9/site-packages/conda/cli/main.py", line 128, in main
return conda_exception_handler(main, *args, **kwargs)
File "/var/lib/miniforge/lib/pypy3.9/site-packages/conda/exception_handler.py", line 388, in conda_exception_handler
return_value = exception_handler(func, *args, **kwargs)
File "/var/lib/miniforge/lib/pypy3.9/site-packages/conda/exception_handler.py", line 20, in __call__
return self.handle_exception(exc_val, exc_tb)
File "/var/lib/miniforge/lib/pypy3.9/site-packages/conda/exception_handler.py", line 51, in handle_exception
from .exceptions import (
File "/var/lib/miniforge/lib/pypy3.9/site-packages/conda/exceptions.py", line 16, in <module>
from requests.exceptions import JSONDecodeError
ImportError: cannot import name 'JSONDecodeError' from 'requests.exceptions' (/opt/slipstream/client/lib/requests/exceptions.py)
Which mamba command is available ?
Using micromamba.
...
BLANCHET Christophe (038eb5bf) at 22 Mar 17:38
Fix the choice of the mamba command (#2).
L'activation de l'environnement base
de conda/mambainterfère avec le client
slipstream`.
install.sh
${MAMBA_BIN} activate base
${MAMBA_BIN} create -y -n napari -c conda-forge python=3.10 napari pyqt
${MAMBA_BIN} deactivate
/var/log/slipstream/client/machine.slipstream.log
Traceback (most recent call last):
File "/var/lib/miniforge/bin/mamba", line 7, in <module>
from mamba.mamba import main
File "/var/lib/miniforge/lib/pypy3.9/site-packages/mamba/mamba.py", line 16, in <module>
from conda.cli.common import check_non_admin, confirm_yn, specs_from_url
File "/var/lib/miniforge/lib/pypy3.9/site-packages/conda/cli/common.py", line 16, in <module>
from ..exceptions import (
File "/var/lib/miniforge/lib/pypy3.9/site-packages/conda/exceptions.py", line 16, in <module>
from requests.exceptions import JSONDecodeError
ImportError: cannot import name 'JSONDecodeError' from 'requests.exceptions' (/opt/slipstream/client/lib/requests/exceptions.py)
Using micromamba to install conda envs solves troubles with the slisptream client.
https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html